Here is my Tuesday column on Colin Kaepernick and the 49ers’ 31st-ranked passing game.

SANTA CLARA – You could argue Colin Kaepernick has been one of the worst starting quarterbacks in the NFL this season.

He definitely has been the worst starting quarterback in the Bay Area. The Raiders’ Terrelle Pryor has outperformed Kaepernick in nearly every statistical category.

Kaepernick was great Week 1 against the Packers but since then Kaepernick has posted Tim-Tebow-like numbers – 50 percent completions and a putrid 62 passer rating over the past four games.

Kaepernick looks disconcerted on the field. He is doing things young quarterbacks do – not going through the full progression, sensing pressure that isn’t there and missing open receivers downfield.

General Manager Trent Baalke flipped over Kaepernick missing an open receiver Week 4 in St. Louis. Baalke was sitting in the Rams’ press box near the writers. There was 1:23 left in the third quarter and the 49ers were winning 21-3. You could say the game was over.

The 49ers had the ball at their 5-yard line and it was second-and-5. Kaepernick faked a handoff to Frank Gore in the end zone, turned around and saw Vernon Davis sprinting wide open downfield on a corner route. Kaepernick stared at Davis and patted the ball twice but didn’t throw it. Instead, he ran to the right and gained 4 yards.

Baalke couldn’t take it. He burst out of his chair. “Throw the ball!” he yelled.

What happened to Kaepernick? Was he fool’s gold? Is he the next Tim Tebow?

No, no, no.

Kaepernick is the real deal. He is the LeBron James of quarterbacks, the most physically talented quarterback ever. The issue is the 49ers’ passing scheme. It lacks rhythm and continuity.

Name the 49ers’ go-to passing play.

You can’t because they haven’t developed one this season.

The 49ers’ offensive philosophy has become simple: Run the ball, or fake the run and chuck it downfield.

The 49ers’ offense wasn’t like this when Alex Smith was the starting quarterback. Jim Harbaugh didn’t seem to trust Smith on downfield throws, so he called shorter passes and the 49ers’ offense was less explosive. On the other hand, Smith never went through a four-game slump under Harbaugh, and the offense went three-and-out much less frequently. The 49ers currently lead the league in that category, going three-and-out on 43 percent of their drives.

The 49ers have Kaepernick throwing the ball more than 20 yards downfield 15 percent of the time, close to the league high. Compare that to Alex Smith, who threw it downfield 8.7 percent of the time last season when he was a 49er, or Peyton Manning, who currently is throwing the ball downfield on 9.1 percent of his passes.

Last season, Kaepernick was the best downfield passer in the NFL. According to Pro Football Focus, his downfield accuracy was 60 percent (counting catches and drops). This season, his downfield accuracy has plummeted to 30 percent. But the 49ers keep making him throw deep 15 percent of the time.

You’d think the 49ers would adjust their play-calling to help Kaepernick end his slump. “I don’t know that we’re going to bang our head into a brick wall all day. We want to give our players a chance to be successful.” That’s what Greg Roman said on Sept. 19 in response to a question concerning his running game. It’s time for him to apply his own advice to his anemic, 31st-ranked passing game.

But Jim Harbaugh seems intent on keeping things the same. On Monday after the Texans game, a reporter asked Harbaugh what is wrong with the passing attack.

“Well, we made some big plays in the passing game.” Defending it.

They made one big play in the passing game – a 64-yard touchdown to Vernon Davis in garbage time. Kaepernick completed six total passes against the Texans. He completed two passes after the first drive of the game.

It is Jim Harbaugh’s and Greg Roman’s job to give Kaepernick a chance to develop continuity and confidence. Harbaugh and Roman must start calling more “small” throws, easy completions, confidence boosters that get other receivers involved and developed as potential weapons.

It is not all about deep passes. The 49ers need to call more slants, more bubble screens, more one-step hitch routes. Let the receiver get yards after the catch like a punt returner. Get him “in space” where he can go one-on-one against a defensive back.

Take the pressure off Kaepernick until he breaks out of his slump. Go back to the basics and re-establish a foundation for the passing offense.

You know, the West Coast Offense. Bill Walsh stuff. Classic 49ers stuff.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat’s website. You can reach him at grantcohn@gmail.com.