KHDC1L

Summary

KHDC1L (KH domain containing 1 like, HGNC:37274) is a protein-coding gene on chromosome 6q13, encoding KHDC1-like protein (Q5JSQ8).

Predicted to enable RNA binding activity and identical protein binding activity. Predicted to be active in cytoplasm.

Source: NCBI Gene 100129128 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_001126063

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37274
Approved symbol	KHDC1L
Name	KH domain containing 1 like
Location	6q13
Locus type	gene with protein product
Status	Approved
Aliases	RP11-257K9.7
Ensembl gene	ENSG00000256980
Ensembl biotype	protein_coding
Entrez	100129128

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000370388, ENST00000471312

RefSeq mRNA: 1 — MANE Select: NM_001126063 NM_001126063

CCDS: CCDS47450

Canonical transcript exons

ENST00000370388 — 3 exons

Exon	Start	End
ENSE00002227844	73223544	73223839
ENSE00002490054	73225297	73225496
ENSE00003666139	73224166	73224348

Expression profiles

Bgee: expression breadth ubiquitous, 111 present calls, max score 89.48.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.1364 / max 728.4244, expressed in 25 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
74350	0.9879	24
74348	0.1114	4
74349	0.0237	3
74346	0.0072	4
74347	0.0062	4

Top tissues by expression

126 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.48	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.99	gold quality
caudate nucleus	UBERON:0001873	75.17	gold quality
nucleus accumbens	UBERON:0001882	73.07	gold quality
right testis	UBERON:0004534	72.86	gold quality
putamen	UBERON:0001874	72.81	gold quality
testis	UBERON:0000473	71.34	gold quality
left testis	UBERON:0004533	71.23	gold quality
cerebellar cortex	UBERON:0002129	64.55	gold quality
cerebellar hemisphere	UBERON:0002245	64.50	gold quality
cerebellum	UBERON:0002037	64.46	gold quality
right hemisphere of cerebellum	UBERON:0014890	62.73	gold quality
brain	UBERON:0000955	61.03	gold quality
placenta	UBERON:0001987	60.63	gold quality
adenohypophysis	UBERON:0002196	59.32	gold quality
substantia nigra	UBERON:0002038	58.84	gold quality
amygdala	UBERON:0001876	58.40	gold quality
temporal lobe	UBERON:0001871	57.96	gold quality
pituitary gland	UBERON:0000007	57.86	gold quality
right frontal lobe	UBERON:0002810	56.84	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	56.82	gold quality
prefrontal cortex	UBERON:0000451	56.81	gold quality
Brodmann (1909) area 9	UBERON:0013540	56.58	gold quality
frontal cortex	UBERON:0001870	56.51	gold quality
anterior cingulate cortex	UBERON:0009835	56.28	gold quality
stromal cell of endometrium	CL:0002255	56.10	gold quality
cerebral cortex	UBERON:0000956	55.99	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	55.90	gold quality
hypothalamus	UBERON:0001898	55.89	gold quality
Ammon’s horn	UBERON:0001954	54.82	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-10018	yes	3581.94
E-MTAB-6819	yes	1654.66
E-MTAB-8060	yes	713.11
E-ANND-3	no	1.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting KHDC1L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-21-5P	99.46	70.54	1035
HSA-MIR-590-5P	99.25	70.76	930
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-6830-3P	98.62	68.07	1760
HSA-MIR-3184-5P	98.56	67.13	1491
HSA-MIR-6511A-3P	97.60	66.61	713
HSA-MIR-6511B-3P	97.60	66.61	713
HSA-MIR-192-3P	97.52	67.66	1001

Literature-anchored findings (GeneRIF, showing 1)

• Upregulation of KHDC1L promotes the proliferation and inhibits apoptosis in head and neck squamous cell carcinoma. (PMID:36734243)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Khdc1c	ENSMUSG00000041722
mus_musculus	Khdc1a	ENSMUSG00000067750
mus_musculus	Khdc1b	ENSMUSG00000085079
rattus_norvegicus	Khdc1	ENSRNOG00000028595
rattus_norvegicus	LOC134483627	ENSRNOG00000063212
rattus_norvegicus		ENSRNOG00000069823

Paralogs (2): KHDC1 (ENSG00000135314), DPPA5 (ENSG00000203909)

Protein

Protein identifiers

KHDC1-like protein — Q5JSQ8 (reviewed: Q5JSQ8)

All UniProt accessions (1): Q5JSQ8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the KHDC1 family.

RefSeq proteins (1): NP_001119535* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031952	MOEP19_KH-like	Domain
IPR036612	KH_dom_type_1_sf	Homologous_superfamily

Pfam: PF16005

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JSQ8-F1	88.76	0.83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): RICKMAN_HEAD_AND_NECK_CANCER_C, SENESE_HDAC3_TARGETS_DN, GAVIN_FOXP3_TARGETS_CLUSTER_P3, DODD_NASOPHARYNGEAL_CARCINOMA_DN, TAVAZOIE_METASTASIS, MIR21_5P, MIR1229_3P, GSE13229_IMM_VS_MATURE_NKCELL_DN, chr6q13, GSE16522_MEMORY_VS_NAIVE_CD8_TCELL_UP, GSE17580_TREG_VS_TEFF_UP, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_24H_ACT_CD4_TCELL_DN, GSE20151_CTRL_VS_FUSOBACT_NUCLEATUM_NEUTROPHIL_DN, GSE20366_TREG_VS_TCONV_UP, GSE20366_EX_VIVO_VS_DEC205_CONVERSION_UP

GO Biological Process (0):

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

150 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KHDC1L	LEUTX	A8MZ59	795
KHDC1L	TRIM43	Q96BQ3	720
KHDC1L	PRAMEF2	O60811	717
KHDC1L	MBD3L2	Q8NHZ7	609
KHDC1L	PRAMEF1	O95521	605
KHDC1L	DUX4L2	P0CJ85	594
KHDC1L	ZSCAN4	Q8NAM6	581
KHDC1L	RFPL4B	Q6ZWI9	544
KHDC1L	ARGFX	A6NJG6	532
KHDC1L	PRAMEF11	O60813	507
KHDC1L	PRAMEF13	Q5VWM6	507
KHDC1L	PRAMEF25	A6NGN4	479
KHDC1L	TRIM48	Q8IWZ4	479
KHDC1L	RFPL2	O75678	478
KHDC1L	TRIM49	P0CI25	475

IntAct

3 interactions, top by confidence:

A	B	Type	Score
KHDC1L		psi-mi:“MI:0915”(physical association)	0.370
SCRIB	CHD2	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A0JNQ6, A6NC42, A6NGQ2, A6NGR9, A6QP75, A7E3N7, A9X185, E1BDF2, E9PGG2, F6SZT2, P0C7A0, P85965, Q06VW1, Q0ZFW8, Q14DK4, Q3UK37, Q3UV16, Q3ZBN4, Q400G9, Q4VXA5, Q587J8, Q5JSQ8, Q60953, Q60I26, Q60I27, Q6NUI2, Q6ZUX3, Q810I0, Q8BH06, Q8C0R7, Q8IWB1, Q8IWY9, Q8IYX4, Q8K4C2, Q8N6L0, Q8N7F7, Q8NCV1, Q8TE82, Q91WA6, Q95JV3

Diamond homologs: P0C7A0, Q3UWR2, Q4KL78, Q4VXA5, Q5JSQ8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

20 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

295 predictions. Top by Δscore:

Variant	Effect	Δscore
6:73224162:CTA:C	donor_loss	1.0000
6:73224163:TA:T	donor_loss	1.0000
6:73224164:A:AC	donor_gain	1.0000
6:73224165:C:CC	donor_gain	1.0000
6:73224165:CCT:C	donor_gain	1.0000
6:73224344:AAGTC:A	acceptor_gain	1.0000
6:73224345:AGTC:A	acceptor_gain	1.0000
6:73224346:GTC:G	acceptor_gain	1.0000
6:73224347:TC:T	acceptor_gain	1.0000
6:73224348:CC:C	acceptor_gain	1.0000
6:73224349:C:A	acceptor_loss	1.0000
6:73224349:C:CA	acceptor_loss	1.0000
6:73224349:C:CC	acceptor_gain	1.0000
6:73224351:G:C	acceptor_gain	1.0000
6:73224351:G:GC	acceptor_gain	1.0000
6:73224356:C:CT	acceptor_gain	1.0000
6:73224358:C:CT	acceptor_gain	1.0000
6:73224359:A:T	acceptor_gain	1.0000
6:73225293:TCA:T	donor_loss	1.0000
6:73225293:TCAC:T	donor_loss	1.0000
6:73225294:CA:C	donor_loss	1.0000
6:73225295:A:AC	donor_gain	1.0000
6:73225295:AC:A	donor_gain	1.0000
6:73225295:ACCGA:A	donor_loss	1.0000
6:73225296:C:A	donor_loss	1.0000
6:73225296:C:CA	donor_gain	1.0000
6:73225296:C:CT	donor_gain	1.0000
6:73225296:CC:C	donor_gain	1.0000
6:73225296:CCG:C	donor_gain	1.0000
6:73225296:CCGA:C	donor_gain	1.0000

AlphaMissense

841 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:73224308:G:C	S51R	0.976
6:73224308:G:T	S51R	0.976
6:73224310:T:G	S51R	0.976
6:73225298:G:C	F37L	0.976
6:73225298:G:T	F37L	0.976
6:73225300:A:G	F37L	0.976
6:73225349:A:C	F20L	0.945
6:73225349:A:T	F20L	0.945
6:73225351:A:G	F20L	0.945
6:73224297:A:G	I55T	0.937
6:73224317:C:A	E48D	0.933
6:73224317:C:G	E48D	0.933
6:73224243:C:T	G73E	0.925
6:73223830:A:G	M102T	0.924
6:73224221:C:A	W80C	0.922
6:73224221:C:G	W80C	0.922
6:73223818:A:T	V106D	0.918
6:73224244:C:G	G73R	0.918
6:73224244:C:T	G73R	0.918
6:73224297:A:C	I55S	0.918
6:73225331:G:C	F26L	0.916
6:73225331:G:T	F26L	0.916
6:73225333:A:G	F26L	0.916
6:73224223:A:G	W80R	0.915
6:73224223:A:T	W80R	0.915
6:73223829:C:A	M102I	0.914
6:73223829:C:G	M102I	0.914
6:73223829:C:T	M102I	0.914
6:73224297:A:T	I55N	0.913
6:73224166:C:G	G99R	0.903

dbSNP variants (sampled 300 via entrez): RS1000240228 (6:73225031 C>A), RS1000574846 (6:73224267 C>T), RS1001573097 (6:73225575 T>C), RS1002190188 (6:73226719 A>G), RS1002521948 (6:73227085 T>C), RS1002579220 (6:73226954 C>T), RS1002649335 (6:73226964 G>A,C), RS1002693753 (6:73223258 T>C), RS1002746084 (6:73223551 C>T), RS1004157948 (6:73227309 T>C), RS1004397290 (6:73226990 A>T), RS1004480992 (6:73226906 C>T), RS1004489499 (6:73226110 T>C,G), RS1004731345 (6:73225740 G>A,C,T), RS1007332860 (6:73225037 C>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression	2
methylmercuric chloride	increases expression	1
systhane	affects response to substance	1
NSC 689534	affects binding, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Copper	affects binding, decreases expression	1
Estradiol	affects response to substance	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.